Merge pull request #1325 from pllim/cubeviz-metadata

ENH: Cubeviz metadata viewer

CHANGES.rst

@@ -14,6 +14,8 @@ Cubeviz
 
 - Cubeviz image viewer now has coordinates info panel like Imviz. [#1315]
 
+- New Metadata Viewer plugin. [#1325]
+
 Imviz
 ^^^^^
 

docs/cubeviz/plugins.rst

@@ -9,6 +9,13 @@ more detail under :ref:`Specviz: Data Analysis Plugins <specviz-plugins>`.  All
 are accessed via the :guilabel:`plugin` icon in the upper right corner
 of the Cubeviz application.
 
+.. _cubeviz-metadata-viewer:
+
+Metadata Viewer
+===============
+
+This plugin allows viewing of any metadata associated with the selected data.
+
 .. _cubeviz-export-plot:
 
 Export Plot

jdaviz/configs/cubeviz/cubeviz.yaml

@@ -17,6 +17,7 @@ toolbar:
   - g-subset-tools
   - g-coords-info
 tray:
+  - g-metadata-viewer
   - g-plot-options
   - g-subset-plugin
   - cubeviz-slice

jdaviz/configs/cubeviz/plugins/parsers.py

@@ -9,6 +9,7 @@
 from specutils import Spectrum1D
 
 from jdaviz.core.registries import data_parser_registry
+from jdaviz.utils import standardize_metadata, PRIHDR_KEY
 
 __all__ = ['parse_data']
 
@@ -45,7 +46,7 @@ def parse_data(app, file_obj, data_type=None, data_label=None):
     #  generic enough to work with other file types (e.g. ASDF). For now, this
     #  supports MaNGA and JWST data.
     if isinstance(file_obj, fits.hdu.hdulist.HDUList):
-        _parse_hdu(app, file_obj, file_name=data_label)
+        _parse_hdulist(app, file_obj, file_name=data_label)
     elif isinstance(file_obj, str) and os.path.exists(file_obj):
         file_name = os.path.basename(file_obj)
 
@@ -68,7 +69,7 @@ def parse_data(app, file_obj, data_type=None, data_label=None):
                     _parse_esa_s3d(app, hdulist, data_label, ext=ext, viewer_name=viewer_name)
 
             else:
-                _parse_hdu(app, hdulist, file_name=data_label or file_name)
+                _parse_hdulist(app, hdulist, file_name=data_label or file_name)
 
     # If the data types are custom data objects, use explicit parsers. Note
     #  that this relies on the glue-astronomy machinery to turn the data object
@@ -82,7 +83,7 @@ def parse_data(app, file_obj, data_type=None, data_label=None):
         raise NotImplementedError(f'Unsupported data format: {file_obj}')
 
 
-def _parse_hdu(app, hdulist, file_name=None):
+def _parse_hdulist(app, hdulist, file_name=None):
     if file_name is None:
         if hasattr(hdulist, 'file_name'):
             file_name = hdulist.file_name
@@ -116,21 +117,25 @@ def _parse_hdu(app, hdulist, file_name=None):
 
         flux = hdu.data << flux_unit
 
+        metadata = standardize_metadata(hdu.header)
+        if hdu.name != 'PRIMARY' and 'PRIMARY' in hdulist:
+            metadata[PRIHDR_KEY] = standardize_metadata(hdulist['PRIMARY'].header)
+
         try:
-            sc = Spectrum1D(flux=flux, wcs=wcs)
+            sc = Spectrum1D(flux=flux, wcs=wcs, meta=metadata)
         except Exception as e:
             logging.warning(e)
             continue
 
         app.add_data(sc, data_label)
 
         # If the data type is some kind of integer, assume it's the mask/dq
-        if hdu.data.dtype in (int, np.uint, np.uint32) or \
-                any(x in hdu.name.lower() for x in EXT_TYPES['mask']):
+        if (hdu.data.dtype in (int, np.uint, np.uint32) or
+                any(x in hdu.name.lower() for x in EXT_TYPES['mask'])):
             app.add_data_to_viewer('mask-viewer', data_label)
 
-        if 'errtype' in [x.lower() for x in hdu.header.keys()] or \
-                any(x in hdu.name.lower() for x in EXT_TYPES['uncert']):
+        if ('errtype' in [x.lower() for x in hdu.header.keys()] or
+                any(x in hdu.name.lower() for x in EXT_TYPES['uncert'])):
             app.add_data_to_viewer('uncert-viewer', data_label)
 
         if any(x in hdu.name.lower() for x in EXT_TYPES['flux']):
@@ -161,11 +166,16 @@ def _parse_jwst_s3d(app, hdulist, data_label, ext='SCI', viewer_name='flux-viewe
         unit = u.Unit(hdulist[ext].header.get('BUNIT', 'count'))
         flux = hdulist[ext].data << unit
     wcs = WCS(hdulist['SCI'].header, hdulist)  # Everything uses SCI WCS
-    data = Spectrum1D(flux, wcs=wcs)
+
+    metadata = standardize_metadata(hdulist[ext].header)
+    if hdulist[ext].name != 'PRIMARY' and 'PRIMARY' in hdulist:
+        metadata[PRIHDR_KEY] = standardize_metadata(hdulist['PRIMARY'].header)
+
+    data = Spectrum1D(flux, wcs=wcs, meta=metadata)
 
     # NOTE: Tried to only pass in sliced WCS but got error in Glue.
     # sliced_wcs = wcs[:, 0, 0]  # Only want wavelengths
-    # data = Spectrum1D(flux, wcs=sliced_wcs)
+    # data = Spectrum1D(flux, wcs=sliced_wcs, meta=metadata)
 
     app.add_data(data, data_label)
     app.add_data_to_viewer(viewer_name, data_label)
@@ -194,7 +204,13 @@ def _parse_esa_s3d(app, hdulist, data_label, ext='DATA', viewer_name='flux-viewe
     wcs = WCS(wcs_dict)
     flux = np.moveaxis(flux, 0, -1)
     flux = np.swapaxes(flux, 0, 1)
-    data = Spectrum1D(flux, wcs=wcs)
+
+    metadata = standardize_metadata(hdulist[ext].header)
+    metadata.update(wcs_dict)  # To be internally consistent
+    if hdulist[ext].name != 'PRIMARY' and 'PRIMARY' in hdulist:
+        metadata[PRIHDR_KEY] = standardize_metadata(hdulist['PRIMARY'].header)
+
+    data = Spectrum1D(flux, wcs=wcs, meta=metadata)
 
     app.add_data(data, data_label)
     app.add_data_to_viewer(viewer_name, data_label)
@@ -225,7 +241,7 @@ def _parse_spectrum1d_3d(app, file_obj, data_label=None):
 
         flux = np.moveaxis(flux, 1, 0)
 
-        s1d = Spectrum1D(flux=flux, wcs=file_obj.wcs)
+        s1d = Spectrum1D(flux=flux, wcs=file_obj.wcs, meta=standardize_metadata(file_obj.meta))
 
         cur_data_label = f"{data_label}[{attr.upper()}]"
         app.add_data(s1d, cur_data_label)

jdaviz/configs/cubeviz/plugins/tests/test_parsers.py

@@ -5,6 +5,8 @@
 from astropy.wcs import WCS
 from specutils import Spectrum1D
 
+from jdaviz.utils import PRIHDR_KEY
+
 
 @pytest.fixture
 def image_hdu_obj():
@@ -58,6 +60,12 @@ def test_fits_image_hdu_parse_from_file(tmpdir, image_hdu_obj, cubeviz_helper):
 
     # This tests the same data as test_fits_image_hdu_parse above.
 
+    cubeviz_helper.app.data_collection[0].meta['EXTNAME'] == 'FLUX'
+    cubeviz_helper.app.data_collection[1].meta['EXTNAME'] == 'MASK'
+    cubeviz_helper.app.data_collection[2].meta['EXTNAME'] == 'ERR'
+    for i in range(3):
+        assert cubeviz_helper.app.data_collection[i].meta[PRIHDR_KEY]['BITPIX'] == 8
+
     flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')
     flux_viewer.on_mouse_or_key_event({'event': 'mousemove', 'domain': {'x': 0, 'y': 0}})
     assert flux_viewer.label_mouseover.pixel == 'x=00.0 y=00.0'
@@ -114,6 +122,7 @@ def test_spectrum1d_parse(spectrum1d, cubeviz_helper):
 
     assert len(cubeviz_helper.app.data_collection) == 1
     assert cubeviz_helper.app.data_collection[0].label.endswith('[FLUX]')
+    assert cubeviz_helper.app.data_collection[0].meta['uncertainty_type'] == 'std'
 
     # Coordinate display is only for spatial image, which is missing here.
     flux_viewer = cubeviz_helper.app.get_viewer('flux-viewer')

jdaviz/configs/default/plugins/metadata_viewer/metadata_viewer.py

@@ -1,8 +1,8 @@
-from astropy.io.fits import Header
 from traitlets import Bool, List, observe
 
 from jdaviz.core.registries import tray_registry
 from jdaviz.core.template_mixin import TemplateMixin, DatasetSelectMixin
+from jdaviz.utils import PRIHDR_KEY, COMMENTCARD_KEY
 
 __all__ = ['MetadataViewer']
 
@@ -11,36 +11,92 @@
 class MetadataViewer(TemplateMixin, DatasetSelectMixin):
     template_file = __file__, "metadata_viewer.vue"
     has_metadata = Bool(False).tag(sync=True)
+    has_primary = Bool(False).tag(sync=True)
+    show_primary = Bool(False).tag(sync=True)
+    has_comments = Bool(False).tag(sync=True)
     metadata = List([]).tag(sync=True)
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         # override the default filters on dataset entries to require metadata in entries
         self.dataset.add_filter('not_from_plugin')
 
+    def reset(self):
+        self.has_metadata = False
+        self.has_primary = False
+        self.show_primary = False
+        self.has_comments = False
+        self.metadata = []
+
     @observe("dataset_selected")
-    def _show_metadata(self, event):
+    def show_metadata(self, event):
         data = self.dataset.selected_dc_item
-        if data is None or not hasattr(data, 'meta') or not isinstance(data.meta, dict) or len(data.meta) < 1: # noqa
-            self.has_metadata = False
-            self.metadata = []
+        if (data is None or not hasattr(data, 'meta') or not isinstance(data.meta, dict)
+                or len(data.meta) < 1):
+            self.reset()
             return
 
-        if 'header' in data.meta and isinstance(data.meta['header'], (dict, Header)):
-            if isinstance(data.meta['header'], Header):  # Specviz
-                meta = dict(data.meta['header'])
-            else:
-                meta = data.meta['header']
+        if PRIHDR_KEY in data.meta:
+            self.has_primary = True
         else:
-            meta = data.meta
+            self.has_primary = False
+            self.show_primary = False
+
+        self.find_public_metadata(data.meta, primary_only=self.show_primary)
+
+    @observe("show_primary")
+    def handle_show_primary(self, event):
+        if not self.show_primary:
+            self.show_metadata(event)
+            return
+
+        data = self.dataset.selected_dc_item
+        if (data is None or not hasattr(data, 'meta') or not isinstance(data.meta, dict)
+                or len(data.meta) < 1):
+            self.reset()
+            return
+
+        self.find_public_metadata(data.meta, primary_only=True)
+
+    def find_public_metadata(self, meta, primary_only=False):
+        if primary_only:
+            if PRIHDR_KEY in meta:
+                meta = meta[PRIHDR_KEY]
+            else:
+                self.reset()
+                return
 
         d = flatten_nested_dict(meta)
-        for badkey in ('COMMENT', 'HISTORY', ''):
+        # Some FITS keywords cause "# ipykernel cannot clean for JSON" messages.
+        # Also, we want to hide internal metadata that starts with underscore.
+        badkeys = ['COMMENT', 'HISTORY', ''] + [k for k in d if k.startswith('_')]
+        for badkey in badkeys:
             if badkey in d:
-                del d[badkey]  # ipykernel cannot clean for JSON
+                del d[badkey]
+
+        if COMMENTCARD_KEY in meta:
+            has_comments = True
+
+            def get_comment(key):
+                if key in meta[COMMENTCARD_KEY]._header:
+                    val = meta[COMMENTCARD_KEY][key]
+                else:
+                    val = ''
+                return val
+        else:
+            has_comments = False
+
+            def get_comment(key):
+                return ''
+
         # TODO: Option to not sort?
-        self.metadata = sorted(zip(d.keys(), map(str, d.values())))
-        self.has_metadata = True
+        public_meta = sorted(zip(d.keys(), map(str, d.values()), map(get_comment, d.keys())))
+        if len(public_meta) > 0:
+            self.metadata = public_meta
+            self.has_metadata = True
+            self.has_comments = has_comments
+        else:
+            self.reset()
 
 
 # TODO: If this is natively supported by asdf in the future, replace with native function.

jdaviz/configs/default/plugins/metadata_viewer/metadata_viewer.vue

@@ -14,18 +14,29 @@
       hint="Select the data to see metadata."
     />
 
+    <v-row v-if="has_primary">
+      <v-switch
+        label="Show primary header"
+        hint="Show MEF primary header metadata instead."
+        v-model="show_primary"
+        persistent-hint>
+      </v-switch>
+    </v-row>
+
     <j-plugin-section-header>Metadata</j-plugin-section-header>
     <div v-if="has_metadata">
       <v-row no-gutters>
         <v-col cols=6><U>Key</U></v-col>
         <v-col cols=6><U>Value</U></v-col>
+        <v-col v-if="has_comments" cols=6><U>Comment</U></v-col>
       </v-row>
       <v-row
         v-for="item in metadata"
         :key="item[0]"
         no-gutters>
         <v-col cols=6>{{ item[0] }}</v-col>
         <v-col cols=6>{{ item[1] }}</v-col>
+        <v-col v-if="has_comments" cols=6>{{ item[2] }}</v-col>
       </v-row>
     </div>
     <v-row v-else>